Package htsjdk.samtools.cram.structure

Enum Class DataSeries

java.lang.Object
java.lang.Enum<DataSeries>
htsjdk.samtools.cram.structure.DataSeries
All Implemented Interfaces:
Serializable, Comparable<DataSeries>, Constable
public enum DataSeries extends Enum<DataSeries>
Represents a specific CRAM record data series and its associated type and unique Content ID. The content id for a data series is not prescribed by the CrAM spec, so the ids used here represent the ID used by this implementation on write. On read, the ID for each data series must be discovered by interrogating the encoding map.

  • Enum Constant Details

    • BF_BitFlags

      public static final DataSeries BF_BitFlags

    • CF_CompressionBitFlags

      public static final DataSeries CF_CompressionBitFlags

    • RI_RefId

      public static final DataSeries RI_RefId

    • RL_ReadLength

      public static final DataSeries RL_ReadLength

    • AP_AlignmentPositionOffset

      public static final DataSeries AP_AlignmentPositionOffset

    • RG_ReadGroup

      public static final DataSeries RG_ReadGroup

    • RN_ReadName

      public static final DataSeries RN_ReadName

    • NF_RecordsToNextFragment

      public static final DataSeries NF_RecordsToNextFragment

    • MF_MateBitFlags

      public static final DataSeries MF_MateBitFlags

    • NS_NextFragmentReferenceSequenceID

      public static final DataSeries NS_NextFragmentReferenceSequenceID

    • NP_NextFragmentAlignmentStart

      public static final DataSeries NP_NextFragmentAlignmentStart

    • TS_InsertSize

      public static final DataSeries TS_InsertSize

    • TL_TagIdList

      public static final DataSeries TL_TagIdList

    • TC_TagCount

      public static final DataSeries TC_TagCount

    • TN_TagNameAndType

      public static final DataSeries TN_TagNameAndType

    • MQ_MappingQualityScore

      public static final DataSeries MQ_MappingQualityScore

    • FN_NumberOfReadFeatures

      public static final DataSeries FN_NumberOfReadFeatures

    • FP_FeaturePosition

      public static final DataSeries FP_FeaturePosition

    • FC_FeatureCode

      public static final DataSeries FC_FeatureCode

    • BB_Bases

      public static final DataSeries BB_Bases

    • QQ_scores

      public static final DataSeries QQ_scores

    • BA_Base

      public static final DataSeries BA_Base

    • QS_QualityScore

      public static final DataSeries QS_QualityScore

    • BS_BaseSubstitutionCode

      public static final DataSeries BS_BaseSubstitutionCode

    • IN_Insertion

      public static final DataSeries IN_Insertion

    • DL_DeletionLength

      public static final DataSeries DL_DeletionLength

    • RS_RefSkip

      public static final DataSeries RS_RefSkip

    • SC_SoftClip

      public static final DataSeries SC_SoftClip

    • PD_padding

      public static final DataSeries PD_padding

    • HC_HardClip

      public static final DataSeries HC_HardClip

    • TM_TestMark

      public static final DataSeries TM_TestMark

    • TV_TestMark

      public static final DataSeries TV_TestMark

  • Method Details

    • values

      public static DataSeries[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static DataSeries valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null

    • getType

      public DataSeriesType getType()

    • getCanonicalName

      public String getCanonicalName()

    • getExternalBlockContentId

      public Integer getExternalBlockContentId()
      The content id for a data series is not prescribed by the CrAM spec, so the ids used here represent the ID used by this implementation on write. On read, the ID for each data series must be discovered by interrogating the encoding map.
      Returns:
      content ID used when writing a CRAM

    • byCanonicalName

      public static DataSeries byCanonicalName(String dataSeriesAbbreviation)
      Return the DataSeries associated with the two-character canonical name
      Parameters:
      dataSeriesAbbreviation - A Data Series canonical name, such as QS for Quality Score
      Returns:
      the associated DataSeries
      Throws:
      CRAMException - for an unknown Data Series